[gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M
msanku65 at yahoo.com
Wed Aug 3 03:20:02 CEST 2011
Hi Justin,
I first performed two minimization using steep and l-bfgs as the method on the
solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized
system ( for each lambda) where essentially same .mdp file was used except the
following change:
gen-vel = yes gen-temp = 280
gen-seed = -1
So, essentially, I heated the minimized system up from 280 K with ref_t 300K
using sd integrator. But, here also I found the average temperature goes to 303
K( instead of 300 K) .
One thing I don't understand that why using md as integrator gives the desired
average temperature( when using Nose-Hoover thermostat) while the sd integrator
does not.
Any further suggestion will be appreciated.
Jagannath
________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tue, August 2, 2011 8:08:20 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M wrote:
> Hi,
> I am trying to calculate the solvation free energy using thermodynamic
>integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem
>in getting accurate average temperature .
> The following is what I did:
> I found that when doing TI, grompp recommends using 'sd' ( stochastic
>dynamics ) as integrator ( provides an warning that for decoupled system, it is
>better to use sd in stead of md ).
> Also I went through Justin Lemkul's tutorial which also recommends using 'sd'
>for TI method. So, I tried to use sd integrator.
>
The tutorial uses BAR for calculation free energy, not TI. Though the protocols
are similar, there is a difference, FYI.
> I wanted to run NVT simulation at 300 K.
> I also found from manual and also from Justin's website on FEP, sd integrator
>implicitly controls temperature and so there is no need to specify a thermostat.
>So, I did not specify any thermostat ( I wrote tcoupl = No ). But,
>unfortunately, I found that after a long simulation , the average temperature
>actually goes to 303 K in stead of 300 K( the desired temperature). This
>happened for all Lambda values where the average temperature turned out to be
>303 K. The .mdp file is pasted at the end of the email and I felt I am using
>reasonable cutoffs and PME as electrostatics.
>
> Here is the output from g_energy command to get the temperature. Statistics
>over 4000001 steps [ 0.0000 thru 8000.0005 ps ], 1 data sets
> All averages are exact over 4000001 steps
>
> Energy Average RMSD Fluct. Drift
Tot-Drift
>
-------------------------------------------------------------------------------
> Temperature 303.333 4.78084 4.78082 5.46937e-06
>0.043755
> Heat Capacity Cv: 12.4764 J/mol K (factor = 0.00024841)
>
>
> I tried three further tests:
> a) I removed tcoupl = No option . But, it is giving same 303K as average
>temperature when using sd.
>
> a) I tried to specify the Nose-Hoover thermostat along with sd. But still, I
>found that when using sd, the average temperature is going to 303 K in stead of
>300 K.
>
>From the manual description of the sd integrator: "The parameter tcoupl is
ignored." This explains (a) and (b).
> c) Finally, I tried to overlook grompp warning and went ahead and used 'md'
>along with Nose-Hoover thermostat. This time I found the right average
>temperature 300 K is being achieved.B
> But, I understand that for a decoupled system like here, I need to use a method
>like stochastic dynamics.
>
> But , I was wondering why it is reaching 303 K in stead of 300 K when using
>sd but 300K is achieved when using md. I looked at the mailing list where
>people had issues with sd and temperature control. But, I could not find a good
>solution. So, any help on the right protocol will be really appreciated.
>
What type of equilibration did you do prior to the data collection? If your
system isn't sampling the desired ensemble, then you shouldn't proceed.
-Justin
>
> Here is my .mdp file.
>
> ; RUN CONTROL PARAMETERS
> integrator = sd
> ; Start time and timestep in ps
> tinit = 0.0
> dt = 0.002
> nsteps = 4000000
> ; For exact run continuation or redoing part of a run
> ; Part index is updated automatically on checkpointing (keeps files separate)
> simulation_part = 1
> init_step = 0
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 1
> ; group(s) for center of mass motion removal
> comm-grps =
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric = 0
> ld-seed = 1993
>
>
>
> ; OUTPUT CONTROL OPTIONS
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 10000
> nstvout = 10000
> nstfout = 0
> ; Output frequency for energies to log file and energy file
> nstlog = 1000
> nstenergy = 10
> ; Output frequency and precision for xtc file
> nstxtcout = 1000
> xtc-precision = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 10
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc = xyz
> periodic_molecules = no
> ; nblist cut-off
> rlist = 1.4
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = pme
> rcoulomb-switch = 0
> rcoulomb = 1.4
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r = 1
> epsilon_rf = 1
> ; Method for doing Van der Waals
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdw-type = shift
> ; cut-off lengths
> rvdw-switch = 1.0
> rvdw = 1.4
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Seperate tables between energy group pairs
> energygrp_table =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 6
> ewald_rtol = 1e-6
> ewald_geometry = 3d
> epsilon_surface = 0
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> tcoupl = No
> ; Groups to couple separately
> tc_grps = System
> ; Time constant (ps) and reference temperature (K)
> tau_t = 1.0
> ref_t = 300
> ; Pressure coupling
> Pcoupl = no
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p = 1.0
> compressibility = 4.5e-5
> ref-p = 1
> ; Scaling of reference coordinates, No, All or COM
> refcoord_scaling = No
> ; Random seed for Andersen thermostat
> andersen_seed = 124821
>
> gen-vel = no
> gen-temp = 300
> gen-seed = -1
>
> ; OPTIONS FOR BONDS
> constraints = hbonds
> ; Type of constraint algorithm
> constraint-algorithm = Lincs
> ; Do not constrain the start configuration
> continuation = yes
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 1e-04
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 12
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 1
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 30
>
> ; Free energy control stuff
> free-energy = yes
> init-lambda = .05
> delta-lambda = 0
> sc-alpha = 0.0
> sc-power = 0
> sc-sigma = 0.0
> couple-moltype = Protein
> couple-lambda0 = vdw
> couple-lambda1 = vdw-q
> couple-intramol = no
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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